Figure 7
Proposed electron/proton-transfer pathways in QFR of D. gigas. The fully reduced manaquinol (MKH2 at the MQ1 site) and the oxidized menaquinone (at the MQ2 site) are shown as yellow sticks. The fully oxidized and semi-oxidized menaquinones are labeled as MK and MKH, respectively. The MK and MKH, newly identified in this work, are bound at the hydrophobic pocket on the C-helix1 (in green). The proposed bifurcation E pathways are labeled with black and orange dot lines and the potential flow pathways of protons generated in the oxidation of MKH2 are labeled as purple dotted lines and classified as proton pathways A and B. The redox cofactors, FAD (upper sticks), hemes (bottom sticks) and iron-sulphur clusters (gray and green balls), are shown on the electron transfer pathway. The residues ligating the redox cofactors are labeled black and the proposed proton acceptors are labeled purple. OM and IM stand for the bacteria outer and inner membranes, respectively. Two black lines indicate the inner membrane. The movement of Tyr-C63 is also shown after bound with the MKH with a hydrogen bond.
